Since copy editors no longer do as thorough a job as they once did (even at the big houses), it's necessary to proof your own work carefully. Here's the beginning of a list:
First, run spellcheck. There's no excuse for egregiously misspelled words when we have a neat little tool like spellcheck at our disposal.
Next, go through the whole document, line by line. You will be looking for:
a. Homophones--words that sound alike but are spelled differently. Common examples include the confusion of "their," "there," and "they're," or "elude" and "allude." Work with a dictionary at your elbow (or an Internet connection open to Webster.com ) and when in doubt, check the word in the dictionary.
b. Repetitive language. If your characters grin three times in a sentence, or laugh four times in three paragraphs, change some of the words so that they're smiling or giggling or whatever, or simply use a different action.
c. Bad punctuation. Make sure you know how to punctuate. I'm dismayed by how many beginning authors seem to think most sentences don't require any commas whatsoever. Use commas when necessary-- don't just toss extra clauses into your sentence without setting them off by commas. If you have a compound sentence, you need a comma. However, don't use commas to do the work of semicolons. Yes, I know a lot of houses no longer permit the use of semicolons (why, I have no clue!), but you can't usually use a comma instead. This is not a grammatical sentence: "She thought he was gorgeous, his chest bulged with muscles." When you find such sentences, use a period. Use an and or a but. Recast the sentence. Whatever. But don't rely on the poor little comma to do the work of a semicolon without help.
d. Overused words. As I've said before, mine are "wryly" and "ruefully." God only knows why I love those words so much... I just do. You probably have a love affair with one or two words without even realizing it. Read your manuscript with careful eyes and you'll find those words you love to excess. Delete them or replace them. Don't worry about their feelings...your manuscript will read more smoothly without them.
e. Illogical paragraph breaks. Make sure your paragraphs break in a logical place. I happen to like short paragraphs, having been raised by a writing mother who thought a lot of "white space" on the page was a good idea. Tom Clancy, on the other hand, likes immensely long paragraphs, but his books seem to sell adequately in spite of it *g*. Either way, make sure your paragraphs make sense, and that you're not lumping too many ideas into one paragraph. And be sure that every character's dialogue is set off by a paragraph-- you should never have two characters speaking in the same paragraph.
f. POV shifts. The general rule is one point of view per scene. Some authors (Erin McCarthy is a notable example) can beautifully execute one POV shift in a scene. A few authors manage to shift back and forth repeatedly with elegance and grace, but most of us can't do that without distracting and annoying the reader. Check your work to make sure you haven't unintentionally "head-hopped," switching POV repeatedly during a scene. You don't want the POV to boing back and forth like a pingpong ball.
That's all I can think of right now, but I'd appreciate any suggestions for additions. It's important to remember that as writers, we're responsible for what leaves our desk. Yes, some editor or proofer may screw up your work before it's published-- it does happen, unfortunately-- but at least you'll have the satisfaction of knowing that when it left your desk, it was perfect. And when you send out perfect manuscripts, you have a much higher probability of a perfect published product.